GEO DataSets

(Submitter supplied) The piRNA pathway is a conserved germline-specific small RNA pathway that ensures genomic integrity and continued fertility. In C. elegans and other nematodes, Type-I piRNA precursor transcripts are expressed from >10,000 small, independently regulated genes clustered within two discrete domains of 1.5 and 3.5 MB on Chromosome IV. These large domains likely play a significant role in promoting germline-specific expression of piRNAs, but the underlying mechanisms are unclear. more...

Organism:

Caenorhabditis elegans

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL26672

52 Samples

Download data: BW, TXT

(Submitter supplied) The piRNA pathway is a conserved germline-specific small RNA pathway that ensures genomic integrity and continued fertility. In C. elegans and other nematodes, Type-I piRNA precursor transcripts are expressed from >10,000 small, independently regulated genes clustered within two discrete domains of 1.5 and 3.5 MB on Chromosome IV. These large domains likely play a significant role in promoting germline-specific expression of piRNAs, but the underlying mechanisms are unclear. more...

Organism:

Caenorhabditis elegans

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL26672

6 Samples

Download data: TXT

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.

Organism:

Caenorhabditis elegans

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL26672

64 Samples

Download data

(Submitter supplied) The piRNA pathway is a conserved germline-specific small RNA pathway that ensures genomic integrity and continued fertility. In C. elegans and other nematodes, Type-I piRNA precursor transcripts are expressed from >10,000 small, independently regulated genes clustered within two discrete domains of 1.5 and 3.5 MB on Chromosome IV. These large domains likely play a significant role in promoting germline-specific expression of piRNAs, but the underlying mechanisms are unclear. more...

Organism:

Caenorhabditis elegans

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL26672

6 Samples

Download data: NARROWPEAK

(Submitter supplied) Background. Telomeric small RNAs related to PIWI-interacting RNAs (piRNAs) have been described in various eukaryotes; however, their role in germline-specific telomere function remains poorly understood. Using a Drosophila model, we performed an in-depth study of the biogenesis of telomeric piRNAs and their function in telomere homeostasis in the germline. Results To fully characterize telomeric piRNA clusters, we integrated the data obtained from analysis of endogenous telomeric repeats, as well as transgenes inserted into different telomeric and subtelomeric regions. more...

Organism:

Drosophila melanogaster

Type:

Non-coding RNA profiling by high throughput sequencing

Platforms:

GPL13304 GPL17275

9 Samples

Download data: TXT

(Submitter supplied) Identification of defects in piRNAs and piRNA precursors

Organism:

Caenorhabditis elegans

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL15716

12 Samples

Download data: FASTA

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.

Organism:

Drosophila melanogaster

Type:

Genome binding/occupancy profiling by high throughput sequencing; Expression profiling by high throughput sequencing; Non-coding RNA profiling by high throughput sequencing

Platform:

GPL13304

24 Samples

Download data: BW, TXT, WIG

(Submitter supplied) Small non-coding RNAs that associate with Piwi proteins, called piRNAs, serve as guides for repression of diverse transposable elements in germ cells of Metazoa. In Drosophila, the genomic regions that give rise to piRNAs, the so-called piRNA clusters, are transcribed to generate long precursor molecules that are processed into mature piRNAs. How genomic regions that give rise to piRNA precursor transcripts are differentiated from the rest of the genome and how these transcripts are specifically channeled into the piRNA biogenesis pathway are not known. more...

Organism:

Drosophila melanogaster

Type:

Expression profiling by high throughput sequencing

Platform:

GPL13304

2 Samples

Download data: TXT

(Submitter supplied) Small non-coding RNAs that associate with Piwi proteins, called piRNAs, serve as guides for repression of diverse transposable elements in germ cells of Metazoa. In Drosophila, the genomic regions that give rise to piRNAs, the so-called piRNA clusters, are transcribed to generate long precursor molecules that are processed into mature piRNAs. How genomic regions that give rise to piRNA precursor transcripts are differentiated from the rest of the genome and how these transcripts are specifically channeled into the piRNA biogenesis pathway are not known. more...

Organism:

Drosophila melanogaster

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL13304

2 Samples

Download data: TXT

(Submitter supplied) Small non-coding RNAs that associate with Piwi proteins, called piRNAs, serve as guides for repression of diverse transposable elements in germ cells of Metazoa. In Drosophila, the genomic regions that give rise to piRNAs, the so-called piRNA clusters, are transcribed to generate long precursor molecules that are processed into mature piRNAs. How genomic regions that give rise to piRNA precursor transcripts are differentiated from the rest of the genome and how these transcripts are specifically channeled into the piRNA biogenesis pathway are not known. more...

Organism:

Drosophila melanogaster

Type:

Expression profiling by high throughput sequencing

Platform:

GPL13304

2 Samples

Download data: BW

(Submitter supplied) Small non-coding RNAs that associate with Piwi proteins, called piRNAs, serve as guides for repression of diverse transposable elements in germ cells of Metazoa. In Drosophila, the genomic regions that give rise to piRNAs, the so-called piRNA clusters, are transcribed to generate long precursor molecules that are processed into mature piRNAs. How genomic regions that give rise to piRNA precursor transcripts are differentiated from the rest of the genome and how these transcripts are specifically channeled into the piRNA biogenesis pathway are not known. more...

Organism:

Drosophila melanogaster

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL13304

10 Samples

Download data: TXT

(Submitter supplied) Small non-coding RNAs that associate with Piwi proteins, called piRNAs, serve as guides for repression of diverse transposable elements in germ cells of Metazoa. In Drosophila, the genomic regions that give rise to piRNAs, the so-called piRNA clusters, are transcribed to generate long precursor molecules that are processed into mature piRNAs. How genomic regions that give rise to piRNA precursor transcripts are differentiated from the rest of the genome and how these transcripts are specifically channeled into the piRNA biogenesis pathway are not known. more...

Organism:

Drosophila melanogaster

Type:

Expression profiling by high throughput sequencing

Platform:

GPL13304

2 Samples

Download data: BW

(Submitter supplied) Small non-coding RNAs that associate with Piwi proteins, called piRNAs, serve as guides for repression of diverse transposable elements in germ cells of Metazoa. In Drosophila, the genomic regions that give rise to piRNAs, the so-called piRNA clusters, are transcribed to generate long precursor molecules that are processed into mature piRNAs. How genomic regions that give rise to piRNA precursor transcripts are differentiated from the rest of the genome and how these transcripts are specifically channeled into the piRNA biogenesis pathway are not known. more...

Organism:

Drosophila melanogaster

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL13304

6 Samples

Download data: WIG

(Submitter supplied) piRNAs play a critical role in the regulation of transposons and other germline genes. In Caenorhabditis elegans, silencing of piRNA target genes is mediated by the Mutator complex, which synthesizes high levels of siRNAs through the activity of an RNA-dependent RNA polymerase. However, how mRNAs recognized by the piRNA pathway are handed off to the Mutator pathway is unclear. Here, we identify the Tudor domain-containing protein, SIMR-1, as a key mediator of this handoff. more...

Organism:

Caenorhabditis elegans

Type:

Expression profiling by high throughput sequencing; Non-coding RNA profiling by high throughput sequencing

Platform:

GPL19757

64 Samples

Download data: TXT

(Submitter supplied) Remarkably, tens of thousands of piwi-interacting RNAs (piRNAs) arise from a minimal number of discrete clustered regions in many organisms. However, it remains unclear if organization into these domains contributes to the highly coordinated, germline-specific expression of these small RNAs. Here, we show that SNPC-4, the DNA-binding subunit of the small nuclear RNA activating protein complex (SNAPc), binds piRNA clusters in a germline-specific manner and is required for global piRNA expression in C. more...

Organism:

Caenorhabditis elegans

Type:

Genome binding/occupancy profiling by high throughput sequencing; Non-coding RNA profiling by high throughput sequencing; Third-party reanalysis

Platform:

GPL9269

14 Samples

Download data: BEDGRAPH, TXT

(Submitter supplied) Piwi proteins and Piwi-interacting RNAs (piRNAs) are best known for their roles in suppressing transposons and promoting fertility. Yet piRNA biogenesis and its mechanisms of action differ widely between distantly related species. To better understand the evolution of piRNAs, we characterized the piRNA pathway in C. briggsae, a sibling species of the model organism C. elegans. Our analyses define 25,883 piRNA producing-loci in C. more...

Organism:

Caenorhabditis briggsae; Caenorhabditis elegans

Type:

Non-coding RNA profiling by high throughput sequencing

Platforms:

GPL18245 GPL21214 GPL29990

12 Samples

Download data: FA

(Submitter supplied) Piwi-interacting RNAs (piRNAs) control transposable element (TE) activity in the germline. piRNAs are produced from single-stranded precursors transcribed from distinct genomic loci, enriched by TE fragments and termed piRNA clusters. The specific chromatin organization and transcriptional regulation of Drosophila germline-specific piRNA clusters ensure transcription and processing of piRNA precursors. more...

Organism:

Drosophila melanogaster

Type:

Non-coding RNA profiling by high throughput sequencing

Platforms:

GPL13304 GPL25244

6 Samples

Download data: TXT

(Submitter supplied) Piwi interacting (pi)RNAs repress diverse transposable elements in the germ cells of metazoans and are essential for fertility in both invertebrates and vertebrates. The precursors of piRNAs are transcribed from distinct genomic regions, the so-called piRNA clusters; however, how piRNA clusters are differentiated from the rest of the genome is not known. To address this question, we studied piRNA biogenesis in two Drosophila virilis strains that show differential ability to generate piRNAs from several genomic regions. more...

Organism:

Drosophila virilis

Type:

Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL13313

24 Samples

Download data: BEDGRAPH

(Submitter supplied) PIWI-interacting (pi) RNAs provide silencing of transposable elements (TE) in the germline. Drosophila telomeres are maintained by transpositions of specialized telomeric retroelements. piRNAs generated from sense and antisense transcripts of telomeric elements provide telomere length control in the germline. Previously, we have found that antisense transcription of the major telomeric retroelement HeT-A is initiated upstream of the HeT-A sense transcription start site. more...

Organism:

Drosophila melanogaster

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL13304

3 Samples

Download data: TXT

(Submitter supplied) In the male germ cells of eutherian animals, 26–30-nt-long PIWI-interacting RNAs (piRNAs) emerge when spermatocytes enter the pachytene phase of meiosis. These pachytene piRNAs derive from ~100 discrete autosomal loci resemble canonical protein-coding genes and long non-coding RNA-producing genes—they are transcribed by RNA polymerase II, bearing 5´ caps and 3´ poly(A) tails, and their transcripts often contain introns that are removed before nuclear export and processing into piRNAs. more...

Organism:

Macaca mulatta; Mus musculus

Type:

Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing

Platforms:

GPL19057 GPL21120

19 Samples

Download data: BW